Hi Lucas, psl2sam.pl in samtools might be a good starting point (though I guess it's not the complete answer as it does not parse the fasta file): http://samtools.svn.sourceforge.net/viewvc/samtools/trunk/samtools/misc/psl2sam.pl?revision=423&view=markup
You could then convert from sam to bam with samtools. cheers Max On Fri, Jul 30, 2010 at 1:55 AM, Mary Goldman <[email protected]> wrote: > > Hi Lucas, > > In order to see alignment coloring, you need to have the sequence. > WebBlat generates a psl plus a fasta file containing the original > sequence, which is uses to display the alignment. Unfortunately, we do > not support pslx formats as custom tracks. However, if you turn can your > psl file and fasta file into a BAM file, then you should be able to see > all of the alignment coloring available in webBlat. This page should > help you get started: http://genome.ucsc.edu/goldenPath/help/bam.html. > > I hope this information is helpful. Please feel free to contact the > mail list again if you require further assistance. > > Best, > Mary > ------------------ > Mary Goldman > UCSC Bioinformatics Group > > On 7/29/10 11:43 AM, Lucas Swanson wrote: > > Thanks Vanessa. > > > > Is it possible to emulate this sort of display with any of the custom > > track formats available? > > > > I have looked into it somewhat and none of the custom track formats seem > > to support multiple colours in a single track line. > > > > Does webBLAT use pslx formatted data for the tracks it displays in the > > Genome Browser? Can custom tracks be in pslx format? > > > > ~Thanks, > > Lucas > > > > Vanessa Kirkup Swing wrote: > > > >> Dear Lucas, > >> > >> Unfortunately, we don't support this in psl customTracks because the plain > >> psl does not have the necessary information for a detailed alignment, i.e. > >> where every substitution is. > >> > >> Please don't hesitate to contact the mailing list if you have further > >> questions. > >> > >> Vanessa Kirkup Swing > >> UCSC Genome Bioinformatics Group > >> > >> > >> ----- Original Message ----- > >> From: "Lucas Swanson"<[email protected]> > >> To: [email protected] > >> Sent: Tuesday, July 27, 2010 5:55:28 PM GMT -08:00 US/Canada Pacific > >> Subject: [Genome] Custom Tracks Resembling WebBLAT Alignments > >> > >> Hello, > >> > >> When webBLAT is used to align a sequence, and then the alignment is > >> viewed in the Genome Browser, > >> "alignments of nucleotides use color to highlight differences as follows: > >> > >> * *red:* Genome and query sequence have different bases at this > >> position. > >> * *orange:* The query sequence has an insertion (or genome has a > >> deletion / alignment gap) at this point. > >> * *purple:* The query sequence extends beyond the end of the > >> alignment. > >> * *green:* The query sequence appears to have a polyA tail which is > >> not aligned to the genome. > >> > >> Also, when the alignment has gaps for both genome and query sequence, > >> double horizontal lines are drawn." > >> > >> However, if command-line BLAT is used to do the alignment, and then the > >> psl output file added to the Genome Browser as a custom track, all of > >> this colour and double-line information is lost. > >> > >> Is there any way to make a custom track that retains this information in > >> any way? > >> > >> ~Thanks, > >> Lucas Swanson > >> _______________________________________________ > >> Genome maillist - [email protected] > >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > >> > >> > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
